Mega Man misterious wakes up one day in a familiar place. He's on the old destroyed highway that he traveled on way back in Mega Man X1. At the end of the highway he meets up with Vile. After fighting Vile, X is transported back to the Dr. Cain's lab. The computer technician, Middy, explains to X that someone has reprogrammed the main frame computer and has brought old battle data back to life. Selflessly, X allows himself to be digitally projected into the computer to fight the menace (As usual, Zero stays behind to "Fight the mavericks").
     Since you end up playing the game 3 times before you finally finish it, there are many different ways to handle the enemies. I use the order below just based on what I know about Mega Man X and X2. There are only characters from X1 and X2 in this game.
The order of bosses by weapon weakness:
   1. Storm Eagle
   2. Flame Stag
   3. Chill Penguin
   4. Spark Mandrill
   5. Armored Armadillo
   6. Morph Moth
   7. Magna Centipede
   8. Wheel Gator